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I have an HSA. W-2 box 12a is code W. My employer cuts the check for my contribution but the contribution actually comes from my compensation. How do I make TurboTax realize that the contribution is by me, thereby not treating this as taxable?

I’ve spoken with an accountant friend that tells me there is a form that this information is supposed to flow to and be filled out properly (“put here employee or employer contributions”) but I can’t seem to find where I can distinguish between the two in TurboTax.  TurboTax states “Code W represents employer payments to your plan” and treats it as taxable income.  Any guidance would be much appreciated.
    I think what is confusing you is that employer contributions are not necessarily contributions made by your employer.  If you have an automatic deduction set up through your payroll it is treated as a pre-tax deduction and not reported in box 1 on your W-2 (thus not taxable).  The code W denotes the amount of income that has been excluded from Box 1 due to contributions to your HSA.   In turbo tax, the box 12a code W contributions are deducted from your total contributions because they have already had pre-tax treatment.  Any remaining HSA contributions over and above your W2 Box 12a code W contributions (funds you contributed directly to the HSA without running through the payroll) qualify for a tax deduction because they have been made with after tax dollars.
      Code W amounts are not taxable or treated as such by TT, and can not be used for the HSA contribution deduction.

      Only your After-Tax contributions over the Code W amount can be used.

       http://www.irs.gov/publications/p969/ar02.html#en_US_2011_publink1000204020
        that amount.